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How to Use GMDB

 

Comparing MSn spectra of analyte with MSn spectral images of various glycans in GMDB, you can estimate glycan structure of analyte. There are two ways of searching relevant spectral images. One is a query on glycan composition, and the other is on m/z value.

 

In the case of performing a query on glycan composition, click a radio button for "Glycan Composition", and input the numbers of each component monosaccharide unit (Hex, HexNAc, dHex, Pent, HexA, Neu5Ac, Neu5Gc) and modification group (Sulfo, Phospho) in the corresponding boxes. The number of adduct ions is also input in the corresponding boxes. In the case of MALDI-TOF MS of glycans, simply enter "1" in a box of "H+" or "Na+" unless you doped other metal ion to the sample. In the case of no adduct, click a check box of "Null". Labeling group can be chosen from a group list "non-labeled, PA, PB, 2AA, 2AB, AP, PBA, OL". Abbreviations for labeling group are indicated as follows:

 

PA: pyridyl amino

PB: pyrene butylic hydrazide

2AA: 2-amido-benzoic acid

2AB: 2-amido-benzamide

AP: aminopyrene

PBA: pyrene butylamine

OL: alditol

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Next, click a "Search" button.

 

In the case of performing a query on m/z value, click a radio button for "m/z".

Then, input m/z value of a precursor ion of your spectrum. To cover a range of m/z value you want to search, enter an appropriate distance in the box of "tolerance". You can normally find relevant spectral images by entering a number from 0.5 to 1.0 in the "tolerance" box.

fig2.tif

Next, click a "Search" button.

 

Then, "Spectral Database Search Result" window will open, and relevant glycan structures are shown. The stored MSn spectra of the glycans are indicated by a tree-structured list of m/z values of precursor ions. In the case of executing a query on m/z value, relevant precursor ions are highlighted in yellow color. You can choose any data by clicking the m/z value of precursor ion of which you want to see the spectrum. If you want to cancel a selection, simply click the highlighted number. To view your selection, click a button of "Show Spectra".

fig3.tif

fig4.tif

 

 

The spectral images appear with the corresponding glycan strucures in "Spectrum" window. The precursor ions are also indicated at the upper left of the spectra. In the case of MS4 spectra, fragmentation path is also indicated. Spectral images can be magnified by defining a range of display. After inputting an appropriate value for display range, click a "Redraw" button to see magnified spectral images. If you want to print the spectral images, simply click a button of "Print".  

fig5.tif

 

Browsing information in GGDB

 

Information in GMDB can be accessed and viewed with web browsers (Internet Explorer, FireFox, and Safari, etc.).